Rabbits can get bordatella infections of the upper respiratory system. However, the best thing to do is take them in to the vet, as the vet can determine exactly what is causing the runny nose. Runny noses are most commonly a pasturella infection in rabbits, not bordatella. If the vet is able to swab their noses and culture the bacteria, he can determine which bacteria is causing the infection, as well as which antibiotic to use on it. It is very common for many of these bacteria to be highly resistant to most antibiotics, and giving the wrong one can be very dangerous. Rabbits rely heavily on good bacteria in their digestive tracts to digest food, so dosing indiscriminately with an antibiotic can be damaging to these good bacteria. Also, giving the wrong antibiotic can make the bacteria evolve resistance to other antibiotics.
There is another cause of a runny nose in rabbits that I want to mention, and that is tooth problems. The roots of the teeth can grow in strange ways to put pressure on the nasal passages. This often leads to a runny nose, and it can be very serious as infected abscesses can form around these tooth roots, requiring dangerous surgery and putting your rabbit at risk for a systemic bacterial infection such as sepsis.
Do not give any dog medicine without first consulting that list of safe antibiotics angieluv posted. You would need to use that list to calculate the correct dose. I still think it is best to take them to a vet for a culture and antibiotic sensitivity test to be done so that you can treat them in the best, safest way possible.
